Biology subjects

Yang, L.-Y.

Publications and source records attributed to Yang, L.-Y..

4 recordsLinked to original sources

bioRxiv2024

Hsa_circ_0001304 promotes vascular smooth muscle cell autophagy and neointimal hyperplasia through the YTHDF2/mTOR axis

IntroductionAberrant autophagy in vascular smooth muscle cells (VSMCs) is associated with the progression of cardiovascular diseases. Recently, circular RNAs (circRNAs) have gradually been reported to regulate autophagy in VSMCs. ObjectivesThis study aims to investigate the role of hsa_circ_0001304 in VSMC autophagy and its underlying mechanism. MethodsThe combined use of dual-luciferase reporter gene assay, MeRIP-qRT-PCR, RIP-qRT-PCR, etc., was performed to verify the regulatory axis, hsa_circ_0001304/miR-636/YTHDF2/mTOR. Cell autophagy detection was performed to uncover the role of hsa_circ_0001304 on VSMC autophagy. The mouse carotid artery ligation model was conducted to assess the role of hsa_circ_0001304 on vascular neointimal hyperplasia. ResultsHsa_circ_0001304 acts as a sponge for miR-636, leading to an increase in the protein levels of YTHDF2. Subsequently, the YTHDF2 promotes the degradation of mTOR mRNA by binding to the latters m6A modification sites. Thus, by regulating the miR-636/YTHDF2/mTOR axis, hsa_circ_0001304 activates VSMC autophagy, aggravating neointimal hyperplasia. ConclusionOur findings suggest that autophagy-related hsa_circ_0001304 could serve as a novel therapeutic target for neointimal hyperplasia-related cardiovascular diseases. Including spacesOur study documents a novel VSMC autophagy-related circRNA, namely circ-1304, which activates VSMC autophagy through the miR-636/YTHDF2/mTOR axis, thereby exacerbating neointimal hyperplasia. Targeting autophagy-related circ-1304 may contribute to the treatment of neointimal hyperplasia-associated cardiovascular diseases.

molecular biology↗

bioRxiv2021

Discovering Novel Antimicrobial Peptides in Generative Adversarial Network

Due to the growing number of clinical antibiotic resistance cases in recent years, novel antimicrobial peptides (AMPs) can become ideal for next-generation antibiotics. This study trained a deep convolutional generative adversarial network (GAN) with known AMPs to generate novel AMP candidates. The quality of the GAN-designed peptides was evaluated in silico, and eight of them named GAN-pep 1[~]8 were chosen to be synthesized for further experiments. Disk diffusion testing and minimum inhibitory concentration (MIC) determination were used to determine the antibacterial effects of the synthesized GAN-designed peptides. Seven out of the eight synthesized GAN-designed peptides showed antibacterial activities. Additionally, GAN-pep 3 and GAN-pep 8 had a broad spectrum of antibacterial effects. Both of them were also effective against antibiotic-resistant bacteria strains such as methicillin-resistant Staphylococcus aureus (S. aureus) and carbapenem-resistant Pseudomonas aeruginosa (P. aeruginosa). GAN-pep 3, the most promising GAN-designed peptide candidate, had low MICs against all the tested bacteria.

microbiology↗

bioRxiv2020

AI4AMP: Sequence-based antimicrobial peptides predictor using physicochemical properties-based encoding method and deep learning

MotivationAntimicrobial peptides (AMPs) are innate immune components that have aroused a great deal of interest among drug developers recently, as they may become a substitution for antibiotics. However, AMPs discovery through traditional wet-lab research is expensive and inefficient. Thus, we developed AI4AMP, a user-friendly web-server that provides an accurate prediction of the antimicrobial activity of a given protein sequence, to accelerate the process of AMP discovery. ResultsOur results show that our prediction model is superior to the existing AMP predictors. AvailabilityAI4AMP is freely accessible at http://symbiosis.iis.sinica.edu.tw/PC_6/ Contactcylin@iis.sinica.edu.tw

microbiology↗

bioRxiv2020

In silico characteration of GmSOS1 provides a comprehensive understaning for its role in soybean salt tolerance

Plant SOS1 encodes plasma membrane Na+/H+ antiporter, which helps in the exclusion of Na+ and improves plant salt tolerance. However, detailed studies of SOS1 in the important oil crop, soybean (Glycine max), are still lacking. In the present study, we carried out a comprehensive in silico analysis of SOS1 in soybean. Referring to the analysis of physicochemical properties and structural characteristics, the GmSOS1 is an acidic protein with instability and hydrophobicity. Subcellular localization of GmSOS1 supports the presumption that GmSOS1 is a plasma membrane Na+/H+ antiporter. Post-translational modification site prediction indicates 4 amino acids that may be phosphorylated. Further, the protein-protein interaction network and co-functional network signify the potential role of GmSOS1 in salt stress tolerance. Although the interaction between GmSOS1 and GmHKT1 remains elusive, some of the intermediary signaling components of SOS pathway in soybean have been predicted. In addition, in silico expression analysis based on transcriptome datasets using publicly available database revealed that GmSOS1 was differentially expressed in tissues and different times. Due to the analysis of its regulation mechanism, we found transcription factors such as WRKY and ERF as well as three miRNAs can regulate the expression of GmSOS1. Phylogenetic analysis using the homologous amino acid sequence of SOS1s from 26 species was performed to study the conserved motifs among these SOS1 members. Overall, we provide an extensive analysis of the GmSOS1 and it promises the primary basis for the study in development and response to salt tolerance.

plant biology↗